Neotoma: Basics with fossil pollen data


👤Ondřej Mottl

04.07.2025

Prague

Made by Ondřej Mottl🙋


Assistant Professor at Charles University

Head of 🧑‍💻Laboratory of Quantitative Ecology



photo by Vladimír Šigut (CUNI)

Fossil pollen

Pollen: More Than Just an Allergen

Palaeoecology

A window to the past

Art by Milan TvM

A window to the past

Photos by John W. Williams (a,b,r); Steffen Wolters (c,d,f,g); Thomas Giesecke (e); Henry H. Hooghiemstra (h,l,n,o,q); Geoff Hope (i); Feli Hopf (j); Eric Colhoun (k), Sarah Ivory (m), Luciane Fontana (p).

Practical Exercise

What is your experience with fossil pollen data?

03:00

Neotoma

Neotoma Paleoecology Database

Neotoma Paleoecology Database

What does Neotoma store?

  • ‘Raw’ Observations on a variety of different proxies (vertebrates, diatoms, pollen, plant macrofossils, testate amoebae, ostracodes, etc.)
    • number of identified specimens, minimum number of individuals, presence/absence
    • information about individual specimens, such as elements, specimen ID, or isotopic values
  • Taxon names
  • Dates (14C, 210Pb, etc.)
  • Age inferences
  • Derived Variables (e.g July mean temperature, species richness)
  • Image files

Neotoma - spatio-temporal scale

Neotoma Paleoecology Database

Neotoma - data access

Neotoma Paleoecology Database

Neotoma - data access

Three main ways to access data:

Neotoma Explorer

Neotoma API

{neotoma2}

Neotoma Paleoecology Database

Neotoma Explorer

Neotoma Explorer

GUI for searching and downloading data.

Note on practical exercises

image by adiasarahma

Practical Exercise

GOAL: Download a pollen record from Neotoma Explorer.

Neotoma explorer

Your turn!

  • Go to Neotoma explorer
  • Dowload a pollen record from a site of your choice
    • try to specify a region (e.g. Europe) and a time period (e.g. Holocene)
  • Save the record as SCV file

15:00

Neotoma API

Neotoma API

Notoma REST API allows to directly send SQL queries from the Neotoma server.

SQL (server) = Structured Query Language

API = Application Programming Interface

REST APIs Explained

Database structure

The neotoma2 R Package

Database structure

This is how it looks like in reality.

The neotoma2 R Package

Database structure

Our interest is Dataset and Samples.

The neotoma2 R Package

Practical Exercise

GOAL: Get information about a pollen record using Neotoma API.

Neotoma API (swagger interface)

Use /v2.0/data/datasets/{datasetid} endpoint.

Practical Exercise

  • get a datasetid from a pollen record of your choice from Neotoma Explorer
  • Go to Neotoma API (swagger interface)
  • Dowload a JSON pollen record use /v2.0/data/downloads/{datasetid} endpoint and selected datasetid

03:00

Fossil pollen data in R

Practical Exercise

GOAL: Get familiar with {neotoma2} R package.


Materials:

Age-depth model

Age-depth modeling - Why?

To assign age to each depth in a core.

Relict Anthropogenic Ecosystem from the Middle Ages: History of a Salt Marsh from Transylvania

Age-depth modeling - How?

Stock.com/Ja’Crispy | Ascough, SUERC

Age-depth modeling - How

Chrono14

Radiocarbon dates - not a real age

Bchron

Age depth model - example

Bchron

Age-depth modeling - example

Chrono14

Practical Exercise

GOAL: Create an age-depth model using {Bchron} package.


Materials:

Past Vegetation through time

Practical Exercise

Goal: Look at a temporal change of presence of selected taxon.

Work in groups and choose a taxon and region of your interest.

💽Raw R code

20:00

Note of multi-record analysis

art by Milan TvM

Note of multi-record analysis

FOSSILPOL

Outro

Science School of Quantitative Ecology

This presentation is created as part of SSoQE project.

More info at Science School of Quantitative Ecology

Code

😸 Code for this presentartion is available on GitHub